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Data: annotate post-2020 reactions with pathways; port the step that was lost in 2020 #300

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Data: annotate post-2020 reactions with pathways; port the step that was lost in 2020 #300

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f7d6d79
Derive an InChI's formula and charge from its own layers, not from a …
Sep 24, 2026
6e51b7d
Validate protonation rows against what a protonation can do; repair t…
Sep 24, 2026
94b0d1f
Marvin 26.1 bundle: replace the 130 rows that are not protonations
Sep 24, 2026
b2c445e
Marvin 23.4 bundle: replace its 38 impossible rows too, and hold both…
Sep 24, 2026
2f925fd
Run_Marvin_Protonations: gate every row on the invariant as it is wri…
Sep 24, 2026
8a98a54
Document the invariant: README, per-bundle sources.yaml notes, run re…
Sep 24, 2026
eb14fea
Consume exactly one protonation bundle per source in the structure pick
Sep 25, 2026
ab59c97
Regenerate the structure picks from the repaired 26.1 bundle
Sep 25, 2026
4707dce
Regenerate the compound records from the new picks
Sep 25, 2026
2a1ea2b
Refresh pipeline: run the rebalance step, and refresh embedded charge…
Sep 25, 2026
8fc8936
Refresh the reactions against the regenerated compound records
Sep 25, 2026
9243e46
Run report and README: what the rollout exposed, and the class the in…
Sep 25, 2026
89dfd4d
Take a compound's formula and charge from the SMILE row when its InCh…
Sep 25, 2026
bf2c36b
Regenerate the picks and records with the fragment-count rule
Sep 25, 2026
1ad34ad
Refresh the reactions against the re-picked records
Sep 25, 2026
254c1eb
Annotate post-2020 reactions with pathways; port the step that was lost
Sep 25, 2026
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879 changes: 879 additions & 0 deletions Biochemistry/Aliases/Unique_ModelSEED_Reaction_Aliases.txt
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99 changes: 99 additions & 0 deletions Biochemistry/Aliases/Unique_ModelSEED_Reaction_ECs.txt
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